Fix Bio.bgzf file mode check for BytesIO (#4270)

* Simplify detection of open files being in binary mode by reading 0 bytes and checking that the result is b"" in BgzfReader and BgzfWriter.
* Removed an unused variable in BgzfWriter._write_block
* Added tests passing binary and non-binary fileobj arguments to bgzf.BgzfReader and bgzf.BgzfWriter

Bio/bgzf.py

@@ -494,7 +494,7 @@ def _load_bgzf_block(handle, text_mode=False):
 class BgzfReader:
     r"""BGZF reader, acts like a read only handle but seek/tell differ.
 
-    Let's use the BgzfBlocks function to have a peak at the BGZF blocks
+    Let's use the BgzfBlocks function to have a peek at the BGZF blocks
     in an example BAM file,
 
     >>> from builtins import open
@@ -597,8 +597,9 @@ def __init__(self, filename=None, mode="r", fileobj=None, max_cache=100):
             raise ValueError(
                 "Must use a read mode like 'r' (default), 'rt', or 'rb' for binary"
             )
+        # If an open file was passed, make sure it was opened in binary mode.
         if fileobj:
-            if "b" not in fileobj.mode.lower():
+            if fileobj.read(0) != b"":
                 raise ValueError("fileobj not opened in binary mode")
             handle = fileobj
         else:
@@ -798,8 +799,9 @@ def __init__(self, filename=None, mode="w", fileobj=None, compresslevel=6):
         """Initilize the class."""
         if filename and fileobj:
             raise ValueError("Supply either filename or fileobj, not both")
+        # If an open file was passed, make sure it was opened in binary mode.
         if fileobj:
-            if "b" not in fileobj.mode.lower():
+            if fileobj.read(0) != b"":
                 raise ValueError("fileobj not opened in binary mode")
             handle = fileobj
         else:
@@ -817,7 +819,6 @@ def __init__(self, filename=None, mode="w", fileobj=None, compresslevel=6):
     def _write_block(self, block):
         """Write provided data to file as a single BGZF compressed block (PRIVATE)."""
         # print("Saving %i bytes" % len(block))
-        start_offset = self._handle.tell()
         if len(block) > 65536:
             raise ValueError(f"{len(block)} Block length > 65536")
         # Giving a negative window bits means no gzip/zlib headers,

Tests/test_bgzf.py

@@ -13,6 +13,7 @@
 import os
 import tempfile
 from random import shuffle
+import io
 
 from Bio import bgzf
 
@@ -465,6 +466,28 @@ def test_BgzfBlocks_TypeError(self):
                 with self.assertRaises(TypeError):
                     list(bgzf.BgzfBlocks(decompressed))
 
+    def test_reader_with_binary_fileobj(self):
+        """A BgzfReader must accept a binary mode file object."""
+        reader = bgzf.BgzfReader(fileobj=io.BytesIO())
+        self.assertEqual(0, reader.tell())
+
+    def test_reader_with_non_binary_fileobj(self):
+        """A BgzfReader must raise ValueError on a non-binary file object."""
+        error = "^fileobj not opened in binary mode$"
+        with self.assertRaisesRegex(ValueError, error):
+            bgzf.BgzfReader(fileobj=io.StringIO())
+
+    def test_writer_with_binary_fileobj(self):
+        """A BgzfWriter must accept a binary mode file object."""
+        writer = bgzf.BgzfWriter(fileobj=io.BytesIO())
+        self.assertEqual(0, writer.tell())
+
+    def test_writer_with_non_binary_fileobj(self):
+        """A BgzfWriter must raise ValueError on a non-binary file object."""
+        error = "^fileobj not opened in binary mode$"
+        with self.assertRaisesRegex(ValueError, error):
+            bgzf.BgzfWriter(fileobj=io.StringIO())
+
 
 if __name__ == "__main__":
     runner = unittest.TextTestRunner(verbosity=2)